2-118118540-G-T

Position:

• chr2-118118540-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.144 in 152,182 control chromosomes in the GnomAD database, including 1,624 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.14 (1624 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.456

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.16 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.144 AC: 21945 AN: 152064 Hom.: 1620 Cov.: 32

Gnomad AFR AF: 0.163

Gnomad AMI AF: 0.0362

Gnomad AMR AF: 0.117

Gnomad ASJ AF: 0.140

Gnomad EAS AF: 0.109

Gnomad SAS AF: 0.142

Gnomad FIN AF: 0.0812

Gnomad MID AF: 0.150

Gnomad NFE AF: 0.154

Gnomad OTH AF: 0.139

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.144 AC: 21967 AN: 152182 Hom.: 1624 Cov.: 32 AF XY: 0.139 AC XY: 10331 AN XY: 74422

Gnomad4 AFR AF: 0.163

Gnomad4 AMR AF: 0.117

Gnomad4 ASJ AF: 0.140

Gnomad4 EAS AF: 0.110

Gnomad4 SAS AF: 0.142

Gnomad4 FIN AF: 0.0812

Gnomad4 NFE AF: 0.154

Gnomad4 OTH AF: 0.137

Alfa AF: 0.141 Hom.: 2311

Bravo AF: 0.147

Asia WGS AF: 0.127 AC: 442 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.93
DANN	Benign	0.52

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs11673900; hg19: chr2-118876116;